Dear bioc-sig-sequencing,
I would like to annotate chip-seq peaks for the arabidopsis genome. "TSS" and
"Exon" are two of the arguments for the 'getAnnotation' function. The "TSS"
argument succeeded, but the "Exon" argument failed.
...
> arabdset<-useMart(biomart="plant_mart_4", dataset = "athaliana_eg_gene")
Checking attributes ... ok
Checking filters ... ok
> ExonArabAnno<-getAnnotation(arabdset, featureType="Exon")
Error in `rownames<-`(`*tmp*`, value = c("ATCG00010.1-E176369",
"ATMG00010.1-E176520", :
duplicate rownames not allowed
> sessionInfo()
R version 2.11.0 Under development (unstable) (2010-02-28 r51186)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ChIPpeakAnno_1.3.4 org.Hs.eg.db_2.3.6
[3] GO.db_2.3.5 RSQLite_0.8-3
[5] DBI_0.2-5 AnnotationDbi_1.9.4
[7] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.15.11
[9] Biostrings_2.15.22 IRanges_1.5.51
[11] multtest_2.3.0 Biobase_2.7.4
[13] biomaRt_2.3.4
loaded via a namespace (and not attached):
[1] MASS_7.3-5 RCurl_1.3-1 splines_2.11.0 survival_2.35-8
[5] tools_2.11.0 XML_2.6-0
>
Can someone comment?
Thanks,
P. Terry
[email protected]
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